You can greatly simplify this by playing with the record separator. Something like the following:

#!/usr/bin/perl -w
use strict; 
use Sys::Hostname qw(hostname);
use Time::HiRes qw(gettimeofday);
use Fatal qw(open close link unlink);

use constant FORWARD => 0;
use constant SUCCESS_DONTFORWARD => 99;

my $maildir = '/var/spam';  # Maildir to store spam in.

{
    local $/ = "\n\n";
    $_ = <>;

    undef $/
    my $body = <>;
}

exit !/^X-Spam-Flag:\s+YES/m
    ? print($_, $body), FORWARD
    : do {
        my $tph = join ".",
            time(), "$$\_".(gettimeofday)[1],  hostname();

        my $temp = "$maildir/tmp/$tph";
        umask 007; # Name's Bond..
        {
            open my $fh, ">", $temp;
            print $fh $_, $body;
        }

        link $temp, "$maildir/new/$tph";
        unlink $temp;

        SUCCESS_DONTFORWARD;
    };
[download]

Untested..

Makeshifts last the longest.